Is there a way to change Ray Visibility settings of linked objects?
Many properties are defined in the master blend file where all changes should be made. We can't change these properties in a linked file as they are always read from the master.

In most cases the only linked items that we want to modify in a scene file are armatures. To be able to modify an armature we make a proxy of the armature in the linked file (CtrlAltP), this can also be applied to other objects. The drawback of making a proxy of a mesh object is that we loose any modifiers in the proxy.

Apart from loosing modifiers other changes made in the master file will still show up in the linked file, this includes mesh changes, materials, textures, but you can change various properties of a proxy object like Ray Visibility.